Protonated hydrates theoretical studies

Both the experimental and theoretical studies indicate that the interactions between acetic acid and water molecules are more competitive in dilute aqueous solution. However to our knowledge, the specific interactions between acetic acid and water molecules are still not well understood, especially in such as the nature of hydrogen bonding, the bonds networking, the rule in architecture of larger hydration compounds, deprotonation of acetic acid in solution, stability of the hydrated proton, the local structure of its aqueous solution, and so on. In the present work, we have performed ab initio calculations on multi-hydrates (rich water hydration compounds) of acetic acid, and ab initio Car-Parrinello molecular dynamics (CPMD) [20] simulations on acetic acid monomer and water system (at dilute aqueous solution condition) to find something helpful for interpreting the nature of acetic acid aqueous solution. 

An important contribution from the ADMP treatment of water clusters has been the so-called amphiphilic nature, or directional hydrophobicity, of the hydrated proton. Through ADMP treatment of protonated water clusters [24], and through the study of large water-vacuum interface systems [25] using the computationally efficient second generation Multi-State Empirical Valence Bond (MS-EVB2) approach [186,187] it was demonstrated that a protonated species tends to reside on the surface of a water vacuum interface with its lone pairs directed away from the neighboring water molecules. These results have subsequently been confirmed by many experimental [188-191] and theoretical studies [192,193]. 

Theoretical studies on protonated hydrates (PH) are illustrative of the progress realized in theoretical chemistry over several decades. The evolution of such studies is presented. The main methods used (quantum chemistry, Monte Carlo or Molecular Dynamics calculations...) and the problems encountered are briefly recalled. Some of the results obtained are commented. 

This short and very limited review gives an idea of the wide variety and complexity of the problems encountered in the study of protonated hydrates. This selection of topics is illustrative of the new possibilities offered by the present developments of theoretical treatments and shows the progress realised in this field, especially within the last few years. Besides the improvement of the accuracy of some of the methods used, in particular to treat the correlation contribution to the intermolecular energies, other categories of methods of lower accuracy bring other kinds of information. This has been exemplified by the results obtained from Monte Carlo and Molecular Dynamics calculations based on the use of DFT or analytical potentials. Though great care must be taken to the possibility of artefacts due to the approximations included in these treatments, such work is complementary to more accurate determinations. We can expect all these methods to be more and more coupled in the near future. 

Abresch et aL, 1998] and of the lumen-side domain of cytochrome/[Martinez et al., 1996]. Finally, in cytochrome c oxidase, two independent theoretical studies have predicted the hydration of buried cavities implicated in the uptake of protons [Riistama et al, 1997 Hofacker and Schulten, 1998]. Although these water molecules were not resolved in published crystallographic structures of the P. denitrificans [Iwata et al, 1995] and bovine heart [Tsukihara et al, 1996] enzymes, many of them are well-defined in a new structure of the Rb, sphaeroides enzyme [M. Svensson-Ek, personal communication]. Understanding the molecular properties giving rise to proton transport in hydrogen-bonded networks containing water molecules is therefore an important step towards the elucidation of proton-pumping mechanisms. 

Before analysis of the interactions of the nucleic acid bases with the clay minerals in the presence of water and cation one needs to understand the individual interactions of NAs with isolated water and with a cation. Such theoretical study was performed for 1 -methylcytosine (MeC) [139]. The study revealed influence of water and cation in the proton transfer for this compound. This leads to the formation of imino-oxo (MeC ) tautomer. Topology of the proton transfer potential surface and thermodynamics of stepwise hydration of MeCNa+ and MeC Na+ complexes is further discussed. The one dimensional potential energy profile for this process followed by the proton transfer with the formation of hydrated MeC Na+ is presented in Fig. 21.2. One-dimensional potential energy profile for amino-imino proton transfer in monohydrated N1-methylcytosine (this represents the situation when tautomerization is promoted by a single water molecule without the influence of Na+ cation) and for the case of pure intramolecular proton transfer (tautomerization is not assisted by any internal interactions) is also included. The most important features of this profile do not depend on the presence or absence of Na+ cation. All the potential energy curves have local minima corresponding to MeC and MeC. However, the significant difference is observed in the relative position of local minima and transition state, which results in a different thermodynamic and kinetic behavior for all presented cases (see Fig. 21.2). 

AI-water complexes with more than three waters have received less attention because it is believed that such large complexes cannot be directly involved in the tautomerization. Moreover, these complexes are difficult to be spectroscopically assigned due to the complexity of their electronic [11] and vibrational [10] structures. 7AI with four waters was studied by Fohner et al. [27] using ultrafast pump-probe spectroscopy combined with theoretical calculations. Their results revealed that the proton-transfer rate increases compared to that of 7AI with two and three waters. Their deuteration studies provided proof for the occurrence of proton transfer (PT), although it was not conclusively confirmed that the proton transfer resulted in a complete tautomerization of the 7AI monomer. For even bigger clusters of 7AI with five waters, there are no experimental investigations available only a theoretical study was reported on the second hydration shell effect [45]. 

Theoretical study of proton transfer in hypoxanthine tautomers Effects of hydration ... 

Aside from NH4" and apart from the pioneer work on the hydrates (Newton and Ehrenson, 1971), few non-metal positive ions have been studied as extensively by theoretical computations. Very recently, calculations have been done on the proton solvation by methanol and dimethylether (Hirao et d., 1982), and N2, CO and O2 (Yamabe, 1981). In our laboratory, a study of the hydrates of NO" in view of understanding the mechanism of production of NO2H is in progress (Pullman and Ranganathan, 1984). 

Geminate recombinations and spur reactions have been widely studied in water, both experimentally and theoretically [13-16], and also in a few alcohols [17,18]. Typically, recombinations occur on a timescale of tens to hundreds of picoseconds. In general, the primary cation undergoes a fast proton transfer reaction with a solvent molecule to produce the stable solvated proton and the free radical. Consequently, the recombination processes are complex and depend on the solvent. The central problem in the theory of geminate ion recombination is to describe the relative motion and reaction between the two particles with opposite charges initially separated by a distance rg. In water, the primary products of solvent radiolysis are the hydrated electron e ", the hydroxyl radical OH and the hydronium cation H3O+ ... 

---